Structure of Homopolymer DNA-CNT Hybrids - PowerPoint PPT Presentation

1 / 26
About This Presentation
Title:

Structure of Homopolymer DNA-CNT Hybrids

Description:

Structure of Homopolymer DNA-CNT Hybrids Suresh Manohar, Tian Tang* *University of Alberta (Canada) What governs the structure of DNA-CNT? Is there an optimal ... – PowerPoint PPT presentation

Number of Views:111
Avg rating:3.0/5.0
Slides: 27
Provided by: Sure97
Category:

less

Transcript and Presenter's Notes

Title: Structure of Homopolymer DNA-CNT Hybrids


1
Structure of Homopolymer DNA-CNT Hybrids
  • Suresh Manohar, Tian Tang
  • University of Alberta (Canada)

2
What governs the structure of DNA-CNT?Is there
an optimal wrapping geometry?
(ns)
  • Contributing Terms in the formation of hybrid
  • Adhesion
  • Entropy loss of DNA backbone
  • Electrostatics
  • Bending and torsion of DNA backbone
  • Deformation of CNT
  • Base-Base Stacking
  • Hydrogen bonding


3
Contributions to the Binding Energy
Contributing Term Estimate (kT/nm for a 1-nm tube)
1 Base-CNT Adhesion 13-35 (based on base-graphite adsorption data)
2 Entropic free energy increase due to chain confinement 0.4 1.3
3 Electrostatics 1.8 3.8 (100 mM salt)
4 Enthalpy increase due to DNA/CNT deformation Negligible for DNA and for CNTs lt 1 nm in diameter
5 Base-base stacking Order of base-CNT adhesion, absorbed into it.
6 Hydrogen bonding Potentially very important sequence dependent (upto 28 kT for GC in vacuum). Negligible for cases studied here.
4
DNA on the nanotube strong binding
  • Nucleotide base adsorption on inorganic surfaces
    (graphite in particular)

Vdw stacking interactions Hydrophobic
interactions Interfacially enhanced hydrogen
bonding

Sowerby et al. PNAS (2001)
Edelwirth et al. Surface Science 1998 Sowerby et
al. Biosystems 2001
5
Contribution due to nanotube deformability can
be neglected for small-diameter tubes
6
Bending/Twisting ssDNA
Very small null Kuhn length? Large effective
Kuhn length at low ionic strength long range
electrostatic repulsion Enthalpic effects?
Bustamante, Bryant, Smith Nature, 421 423 (2003)
7
Entropy Loss Due to Backbone Confinement
  • Order of kbT per nm (and smaller at low ionic
    strength)
  • Important at high ionic strength
  • Negligible at low ionic strength

8
Enthalpic terms (stretch, bend, twist)
negligible!
Small null Kuhn length!

9
Electrostatics
  • Line of Charges Interacting Through the
    Debye-Huckel Potential
  • Account for nonlinearity using Manning
    Condensation

100 mM monovalent salt (T 300K), 1.8 3.8
per nm
10
Contributions to the Binding Energy
Contributing Term Estimate (kT/nm for a 1-nm tube)
1 Base-CNT Adhesion 13-35 (based on base-graphite adsorption data)
2 Entropic free energy increase due to chain confinement 0.4 1.3
3 Electrostatics 1.8 3.8 (100 mM salt)
4 Enthalpy increase due to DNA/CNT deformation Negligible for DNA and for CNTs lt 1 nm in diameter
5 Base-base stacking Order of base-CNT adhesion, absorbed into it.
6 Hydrogen bonding Potentially very important sequence dependent (upto 28 kT for GC in vacuum). Negligible for cases studied here.
11
Molecular Dynamics (MD) Simulation
  • MD was done using CHARMM program and forcefield.
  • Systematic study of poly(T) with 12 bases around
    (10,0) CNT.
  • CNT interacts with other atoms through vdw
    interactions only.
  • PME Method was used.

12
Equilibration


Minimized
Equilibrated at 300K
Pitch 17.7 nm
13
Phosphate Group Solvated

Location of P atoms (for DNA with helical pitch
of 61.5 nm). Yellow Starting loactions Red
Final locations P distance 9.8 0.5 Å from CNT
axis
Solvated P atoms. Blue P atoms
14
Several Bases Un-Stack

Unstacked BAse
Stacked Base
Stacked Base is at a distance of 3.45 Å from CNT
surface Water envelope starts at a distance of
6.8 0.5 Å from CNT axis
15
Unstacking of Bases
16
Reduction of Effective Adhesion Energy
a 35o stacked base a gt 35o unstacked base
W Adhesion energy for single base WAdenine
-7.8 kcal/mol WThymine -6.3 kcal/mol A gt T
? Adhesion energy of base in chain ?Adenine
-2.4 kcal/mol ?Thymine -3.3 kcal/mol Poly-dT gt
Poly-dA
17
Lateral Mobility of Base



Mean bond length for T base 1.39 Ao Energy
Barrier 2 kBT
Projection of nearest CNT carbon atom onto base
plane
18
Kuhn Length

lk, Kuhn length 5 nm for poly-dT on CNT surface
19
Analytical Model
Pitch 2pc a 9 Ao, d 2 Ao, d 7 Ao e1 80,
e2 1 Q -1.609 e-19 C
  1. At low ionic strengths, the competition between
    electrostatics and effective adhesion lead to an
    optimal wrapping geometry.
  2. Free energy due to adhesion, Gad -l?, where l
    is the arc length of DNA per unit length of CNT,
    ? is the adhesion energy per unit arc length of
    DNA.
  3. Electrostatics is handled using counterion
    condenstaion theory.

20
Sum charge-charge interactions on a HelixApply
counterion-condensation theory
g gad gel
Free energy of hybrid,
21
For low-ionic strength, competition between
electrostatics adhesion gives an optimal
helical wrap
22
Summary
  • Scaling analysis, molecular dynamics and an
    analytical model were used to study the hybrid.
  • At low limit of ionic strengths, competition
    between electrostatics and adhesion leads to
    optimum wrapped geometry.
  • Poly-dT adheres better than poly-dA even though
    AgtT for single bases.

23
Methodology
  • Starting structure was created in Materials
    StudioTM (MS).
  • Sodium ions placed at a distance of 3.5 Å from P
    atoms.
  • A pre-equilibrated water box of dimension
    102x39x33 Å3 was used.
  • The solute (DNACNTions) was placed at the
    center of water box.
  • Periodic boundary conditions were employed using
    CRYSTAL command in CHARMM.
  • Initial structure was minimized for 500 steps
    using Newton Raphson.
  • Two stage heating and equilibration done in NPT
    ensemble.
  • 400 ps production phase done in NVT ensemble.
  • This procedure was followed for structures with
    varying helical pitches.

24
Scheme for AFM experiment
Gold coated AFM tip
Attach thiolated ssDNA to the tip
Do Force Measurements on samples with Graphite or
CNT in water
Get Force-Deflection plot
Extract pull-off force and adhesion energy
25
CNT Sample in water
Graphite in water
Force plot for Au tip on graphite in water
Force plot for (DNA 2-mercaptoethanol) tip on
graphite in water
26
  • Ongoing Work
  • AFM experiments.
  • Molecular simulations to estimate the binding
    free energy between Graphite/CNT and single DNA
    base (A,T,C,G) using Thermodynamic Integration
    and Density of States method.
Write a Comment
User Comments (0)
About PowerShow.com